Well, for best instant in stock, Feather Craft is definitly the best in town. However, my favorite is Hargrove. Is he doesnt have it, he will order it for me and i'll get it 2-3 days later. I've been going to his shop for 14 years now and there is never anything I need in an absolute hurry and if I must have it, i will snag some from his tying bench and pay em back later.
For online stores I'd go with Caster's Fly Shop. They have a great selection and service, and free shipping! For me that's a great bonus especially when placing a smaller order. Check out Dave, the owner's, fly patterns.
Never will find everything under one roof, especially if you're a "discriminating" tier (my family call me impossible). For online, Great Feathers in MD for Pearsall's, Kamasan and Grip(also stock Cookshill feathers), Dette's for Whiting Capes and interesting feathers for the exotic salmon tier, Steve Cooper at Cookshill in the UK for game skins and feathers, and I just put in an order with Finney's flies in Ireland. I prefer buying feathers where I know the quality is outstanding.
Fly Fishing Specialties out of Citrus Heights, California, has the best selection in Northern California. I used to write the materials orders for the shop. Trust me, maintaining the material inventory was a major task.
In regards to all of California, some of my former colleagues in the industry told me, only Bob Marriotts in Fullerton may have more inventory.
Not to get confused with my old digs, there is an online fly shop called flytyingspecialties.com. It is operated by a great guy named Steve Korbay. He usually stocks some hard to find materials. He is hardcore into the Czech nymphing scene.